[gmx-users] position restraint and pdb

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 8 08:27:00 CET 2008

Bhawana Gupta wrote:
> hello everyone,
> pls tell me that whether we can use gromacs for simulating pdb with 3 or 
> 4 residue.

Yes. You can use GROMACS to simulate traffic if you want to. :-)

> As i had done it with 4 residue with blocking group. But then i got the 
> error for rvdw and rlist as they should be nearer to cutoff value.
> So instead of decreasing the value of rvdw. i increased my X, Y, Z 
> coordinates.
> Tell me whether i m correct or not.

We can't possibly tell because we don't know
a) your objective and
b) what sizes you've tried, and
c) what force field you're trying to use, and
d) what errors you've received and
e) what other problems you've encountered.
f) how you've tried to solve the above.

Please read the contents of http://wiki.gromacs.org/index.php/Support 
and consider how you can better use the resources of people who might be 
prepared to help you. Remember, it's not our job to do so, and 
frustrated though you might be, you need to work hard to interact 
successfully with the mailing list too.

rcoulomb and rvdw should stay close to the values used for 
parameterizing that force field. If you don't know what they are, go and 
read up.

> One more thing
> whether we can apply position restraint to all the atoms in the 
> file.whether it will have any impact on my output.
> Silly Ouestion. But sorry for that.

Yes you can. But then you will have dynamics subject to position 
restraints. That's not usually a useful thing.

> How we can come to know that to which atom i add position restraint in 
> posre.itp file.Sorry i don't Know about this
> I read the manual but i m confused.

The format of the [ position_restraints ] section is explained in 
chapter 5. There's an example there. The underlying maths is in chapter 
4. It's really not that hard.

Have you done all of the tutorial material you can find? This will teach 
you some of the normal ways of doing things. It's much easier to make up 
your protocol to suit your objectives once you've seen a range of things 


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